Jeffrey Ouyang-Zhang

Btw, if you hate your PhD you can just leave. You can transfer (I did), you can drop out. More people probably should.

First they came for Columbia...

ooh also very curious 👀

Could you add me to this list?

Implementation is extremely simple. If you are using ESM2, you're just one line of code away from upgrading to ISM's enhanced capabilities. (7/7)
🔖 paper www.biorxiv.org/content/10.1...
💻 github: github.com/jozhang97/ISM
🤗 huggingface: huggingface.co/jozhang97/is...

To conclude, ISM takes sequence-only input but produces structurally-rich representations. After all, the amino acid sequence is the only genetic information necessary for protein folding. Our structural loss better enables transformers to learn sequence-structure mapping. (6/7)

On structural benchmarks, we found that our model's structural representations outperform those from existing sequence models and even match performance with representations from models that take structure and sequence as input. (5/7)

ISM's secret sauce is a microenvironment-based autoencoder. The all-atom autoencoder learns to embed the tertiary structure surrounding a residue into a structure token. We distill these per-residue tokens (and MutRank tokens) into ESM2. (4/7)

Masked language modeling enables ESM2 to learn rich evolutionary features which capture a view of the structural landscape. However, it often underperforms structure models on downstream tasks.

We fine-tune ESM2 to predict representations from structure models. (3/7)

ISM is our latest protein language model which enhances ESM2 with enriched structural representations. (2/7)

Are you using ESM2 for your sequence embeddings? Try out ISM, a one-line code change that will incorporate improved structure and sequence information, without a structure as input. (1/7)